Identification of functional genomic regions with copy number alteration in liver cancer

Tzu Hung Hsiao; Hung I.Harry Chen; Yidong Chen

doi:10.1109/GENSIPS.2012.6507752

Identification of functional genomic regions with copy number alteration in liver cancer

Tzu Hung Hsiao, Hung I.Harry Chen, Yidong Chen

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

1 Scopus citations

Abstract

Copy number alterations (CNAs) happen frequently in solid tumors. Several oncogenes and tumor suppressor genes have been identified with CNAs. However, the systematic survey of CNA regulated functions is still lack. By employing systems biology approaches, instead of examining individual genes, we directly identified the spatial functional hotspots in human genome. Total 249 genomic regions, or segments, with 410 enriched biological functions were identified. An aCGH data set of hepatocellular carcinoma (HCC) tumors was employed in this study and several putative affected functions of CNAs were identified. Our results indicate that 4 immune related segments were lost in most of patients. In addition, our data implied these immune related segments might be involved in HCC oncogenesis. The result further demonstrated that our method enables researchers to survey biological functions of CNAs and to construct regulation hypothesis at pathway and functional levels.

Original language	English (US)
Title of host publication	Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2012
Pages	155-158
Number of pages	4
DOIs	https://doi.org/10.1109/GENSIPS.2012.6507752
State	Published - 2012
Event	2012 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2012 - Washington, DC, United States Duration: Dec 2 2012 → Dec 4 2012

Publication series

Name	Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics
ISSN (Print)	2150-3001
ISSN (Electronic)	2150-301X

Other

Other	2012 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2012
Country/Territory	United States
City	Washington, DC
Period	12/2/12 → 12/4/12

Keywords

Copy number alteration
gene set enrichment
liver cancer
pathway analysis

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology (miscellaneous)
Computational Theory and Mathematics
Signal Processing
Biomedical Engineering

Access to Document

10.1109/GENSIPS.2012.6507752

Cite this

Hsiao, T. H., Chen, H. I. H., & Chen, Y. (2012). Identification of functional genomic regions with copy number alteration in liver cancer. In Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2012 (pp. 155-158). Article 6507752 (Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics). https://doi.org/10.1109/GENSIPS.2012.6507752

Identification of functional genomic regions with copy number alteration in liver cancer. / Hsiao, Tzu Hung; Chen, Hung I.Harry; Chen, Yidong.
Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2012. 2012. p. 155-158 6507752 (Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Hsiao, TH, Chen, HIH & Chen, Y 2012, Identification of functional genomic regions with copy number alteration in liver cancer. in Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2012., 6507752, Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics, pp. 155-158, 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2012, Washington, DC, United States, 12/2/12. https://doi.org/10.1109/GENSIPS.2012.6507752

Hsiao TH, Chen HIH, Chen Y. Identification of functional genomic regions with copy number alteration in liver cancer. In Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2012. 2012. p. 155-158. 6507752. (Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics). doi: 10.1109/GENSIPS.2012.6507752

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abstract = "Copy number alterations (CNAs) happen frequently in solid tumors. Several oncogenes and tumor suppressor genes have been identified with CNAs. However, the systematic survey of CNA regulated functions is still lack. By employing systems biology approaches, instead of examining individual genes, we directly identified the spatial functional hotspots in human genome. Total 249 genomic regions, or segments, with 410 enriched biological functions were identified. An aCGH data set of hepatocellular carcinoma (HCC) tumors was employed in this study and several putative affected functions of CNAs were identified. Our results indicate that 4 immune related segments were lost in most of patients. In addition, our data implied these immune related segments might be involved in HCC oncogenesis. The result further demonstrated that our method enables researchers to survey biological functions of CNAs and to construct regulation hypothesis at pathway and functional levels.",

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AB - Copy number alterations (CNAs) happen frequently in solid tumors. Several oncogenes and tumor suppressor genes have been identified with CNAs. However, the systematic survey of CNA regulated functions is still lack. By employing systems biology approaches, instead of examining individual genes, we directly identified the spatial functional hotspots in human genome. Total 249 genomic regions, or segments, with 410 enriched biological functions were identified. An aCGH data set of hepatocellular carcinoma (HCC) tumors was employed in this study and several putative affected functions of CNAs were identified. Our results indicate that 4 immune related segments were lost in most of patients. In addition, our data implied these immune related segments might be involved in HCC oncogenesis. The result further demonstrated that our method enables researchers to survey biological functions of CNAs and to construct regulation hypothesis at pathway and functional levels.

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Identification of functional genomic regions with copy number alteration in liver cancer

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